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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ), 'gf_id' => 'HOM05D001554', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001554' ), 'data_identifier' => 'HOM05D001554', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001554', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '411', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12780' => 'bna', 'A02p10560' => 'bna', 'A08p15150' => 'bna', 'A09p25770' => 'bna', 'A10p11260' => 'bna', 'A10p11400' => 'bna', 'Aa31LG3G9920' => 'aar', 'Aa31LG6G3470' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.169' => 'aag', 'Actinidia05148' => 'ach', 'Actinidia09905' => 'ach', 'Actinidia11812' => 'ach', 'Actinidia12459' => 'ach', 'Actinidia18740' => 'ach', 'Actinidia24055' => 'ach', 'Actinidia35284' => 'ach', 'Ah.01g005220' => 'amhyb', 'Ah.04g165370' => 'amhyb', 'Ah.09g236450' => 'amhyb', 'Ah.14g088870' => 'amhyb', 'AL6G48660' => 'aly', 'AL6G48920' => 'aly', 'AL7G32610' => 'aly', 'AL8G29240' => 'aly', 'Aqoxy1G03899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.67WLF9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8XPP8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BVMI19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LGR9JS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PRT3GM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WFJ76T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX0MPJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHX78I' => 'arhy', 'AT4G05060' => 'ath', 'AT4G21450' => 'ath', 'AT5G54110' => 'ath', 'ATR0691G133' => 'atr', 'ATR0693G235' => 'atr', 'Atru.chr10.2020' => 'acertr', 'Atru.chr2.2927' => 'acertr', 'Atru.chr6.3080' => 'acertr', 'AUR62012485' => 'cqu', 'AUR62014710' => 'cqu', 'AUR62015589' => 'cqu', 'AUR62029302' => 'cqu', 'BcaB01g01866' => 'bca', 'BcaB03g11692' => 'bca', 'BcaB05g22112' => 'bca', 'BcaB08g35761' => 'bca', 'BcaC01g00696' => 'bca', 'BcaC03g14324' => 'bca', 'BcaC03g14325' => 'bca', 'BcaC04g20391' => 'bca', 'BcaC04g21367' => 'bca', 'BcaC09g51219' => 'bca', 'BcaNung02796' => 'bca', 'BolC1t01492H' => 'bol', 'BolC2t07893H' => 'bol', 'BolC3t20611H' => 'bol', 'BolC9t56110H' => 'bol', 'BolC9t57292H' => 'bol', 'BraA01t01221Z' => 'bra', 'BraA02t06120Z' => 'bra', 'BraA08t33495Z' => 'bra', 'BraA09t38146Z' => 'bra', 'BraA10t43234Z' => 'bra', 'C01p15380' => 'bna', 'C02p17620' => 'bna', 'C03p83300' => 'bna', 'C09p32640' => 'bna', 'C09p44200' => 'bna', 'CAN.G162.109' => 'can', 'CAN.G424.24' => 'can', 'CAN.G443.8' => 'can', 'CAN.G508.13' => 'can', 'CANSAT11G1246' => 'cansat', 'CANSAT64G0206' => 'cansat', 'CARHR228130' => 'chi', 'CARHR252490' => 'chi', 'CARHR267310' => 'chi', 'Carub.0006s3303' => 'cru', 'Carub.0007s1998' => 'cru', 'Carub.0008s1440' => 'cru', 'Ca_01538_v3' => 'car', 'Ca_01798_v3' => 'car', 'Ca_18476_v3' => 'car', 'Cc02_g12350' => 'ccan', 'Cc05_g06180' => 'ccan', 'Cc05_g06250' => 'ccan', 'Cc05_g12760' => 'ccan', 'CDE01G0605' => 'cde', 'CDE02G2086' => 'cde', 'CDE05G0102' => 'cde', 'CDE05G0477' => 'cde', 'CDE12G0494' => 'cde', 'Cfa000345' => 'cfa', 'Cfa014540' => 'cfa', 'Cfa020498' => 'cfa', 'Ciclev10009203m.g' => 'ccl', 'Ciclev10016218m.g' => 'ccl', 'Ciclev10016298m.g' => 'ccl', 'CiPaw.03G169500' => 'cil', 'CiPaw.04G122500' => 'cil', 'CiPaw.10G117800' => 'cil', 'CiPaw.11G177600' => 'cil', 'CiPaw.12G123400' => 'cil', 'ClCG01G022500' => 'cla', 'ClCG02G017300' => 'cla', 'ClCG11G018560' => 'cla', 'COL.COLO4_09490' => 'col', 'COL.COLO4_13646' => 'col', 'COL.COLO4_31596' => 'col', 'Cpa.g.sc1178.1' => 'cpa', 'Cpa.g.sc12.35' => 'cpa', 'Cpa.g.sc34.86' => 'cpa', 'CsaV3_3G044310' => 'csa', 'CsaV3_6G012370' => 'csa', 'CsaV3_6G012380' => 'csa', 'CsaV3_6G012400' => 'csa', 'CsaV3_6G049670' => 'csa', 'CSS0012220' => 'camsi', 'CSS0029752' => 'camsi', 'CSS0032137' => 'camsi', 'CSS0033310' => 'camsi', 'CSS0033629' => 'camsi', 'DCAR_004149' => 'dca', 'DCAR_008080' => 'dca', 'DCAR_008082' => 'dca', 'DCAR_022491' => 'dca', 'Dinv08351' => 'din', 'Dinv15498' => 'din', 'Dinv18986' => 'din', 'Dinv22358' => 'din', 'Dinv40472' => 'din', 'Duzib052G1184' => 'dzi', 'Duzib132G0762' => 'dzi', 'Duzib160G0430' => 'dzi', 'Duzib170G0560' => 'dzi', 'Duzib192G0247' => 'dzi', 'Duzib213G0059' => 'dzi', 'Duzib235G0596' => 'dzi', 'Duzib248G1202' => 'dzi', 'Duzib268G0425' => 'dzi', 'ECA234G0184' => 'eca', 'ECA236G0462' => 'eca', 'ECA240G1883' => 'eca', 'ECA248G2198' => 'eca', 'EL10Ac4g08046' => 'bvu', 'EL10Ac8g20540' => 'bvu', 'Eucgr.D00750' => 'egr', 'Eucgr.F01073' => 'egr', 'Eucgr.K00911' => 'egr', 'FAN02G3363' => 'fan', 'FAN05G2599' => 'fan', 'FAN09G0651' => 'fan', 'FAN11G0761' => 'fan', 'FAN11G4017' => 'fan', 'FAN14G1911' => 'fan', 'FAN16G0268' => 'fan', 'FAN16G2464' => 'fan', 'FAN21G0106' => 'fan', 'FAN21G1780' => 'fan', 'FAN25G2591' => 'fan', 'FAN25G2960' => 'fan', 'FvH4_3g03880' => 'fve', 'FvH4_3g21120' => 'fve', 'FvH4_6g44480' => 'fve', 'Glyma.06G298500' => 'gma', 'Glyma.07G189400' => 'gma', 'Glyma.08G059800' => 'gma', 'Glyma.12G106750' => 'gma', 'Glyma.12G106800' => 'gma', 'Glyma.12G200900' => 'gma', 'Glyma.12G218700' => 'gma', 'Glyma.13G246800' => 'gma', 'Glyma.13G282300' => 'gma', 'Glyma.13G301300' => 'gma', 'Glyma.15G067100' => 'gma', 'Gohir.A01G069200' => 'ghi', 'Gohir.A05G166100' => 'ghi', 'Gohir.A06G127400' => 'ghi', 'Gohir.A10G021600' => 'ghi', 'Gohir.A13G057000' => 'ghi', 'Gohir.D01G056700' => 'ghi', 'Gohir.D04G111266' => 'ghi', 'Gohir.D05G169100' => 'ghi', 'Gohir.D05G328400' => 'ghi', 'Gohir.D06G127900' => 'ghi', 'Gohir.D10G022400' => 'ghi', 'Gohir.D11G227940' => 'ghi', 'Gohir.D13G064900' => 'ghi', 'Gorai.002G076800' => 'gra', 'Gorai.009G174300' => 'gra', 'Gorai.010G149600' => 'gra', 'Gorai.011G023500' => 'gra', 'Gorai.013G073700' => 'gra', 'GSVIVG01003659001' => 'vvi', 'GSVIVG01014445001' => 'vvi', 'GSVIVG01030002001' => 'vvi', 'HanXRQChr02g0031361' => 'han', 'HanXRQChr05g0131141' => 'han', 'HanXRQChr05g0131181' => 'han', 'HanXRQChr05g0144291' => 'han', 'HanXRQChr16g0517481' => 'han', 'Haze_06586' => 'cav', 'Haze_09544' => 'cav', 'Haze_13079' => 'cav', 'Hma1.2p1_0662F.1_g198290' => 'hma', 'Hma1.2p1_1176F.1_g264160' => 'hma', 'Hma1.2p1_1182F.1_g264780' => 'hma', 'Hma1.2p1_1571F.1_g291310' => 'hma', 'Hma1.2p1_1579F.1_g291860' => 'hma', 'Hma1.2p1_2163F.1_g315700' => 'hma', 'HPP92_012361' => 'vpl', 'HPP92_014082' => 'vpl', 'HPP92_016550' => 'vpl', 'Hund08049' => 'sun', 'Hund12777' => 'sun', 'Hund21281' => 'sun', 'Hund23370' => 'sun', 'Hund23601' => 'sun', 'Lalb_Chr01g0017061' => 'lal', 'Lalb_Chr03g0029141' => 'lal', 'Lalb_Chr05g0218131' => 'lal', 'Lalb_Chr09g0327271' => 'lal', 'Lalb_Chr19g0135511' => 'lal', 'Lj1A854T35' => 'lonja', 'Lj2A279T54' => 'lonja', 'Lj3g0003030' => 'lja', 'Lj3g0014813' => 'lja', 'Lj4g0010294' => 'lja', 'Lj8C118T7' => 'lonja', 'Lsat_1_v5_gn_1_122940' => 'lsa', 'Lsat_1_v5_gn_4_56520' => 'lsa', 'Lsat_1_v5_gn_7_105960' => 'lsa', 'Lsat_1_v5_gn_7_20680' => 'lsa', 'Manes.03G117100' => 'mes', 'Manes.12G082500' => 'mes', 'Manes.15G082400' => 'mes', 'Manes.16G020000' => 'mes', 'Manes.17G033500' => 'mes', 'Mapoly0039s0107' => 'mpo', 'MBI02_g13227_MAGBIO' => 'mbi', 'MBI18_g27683_MAGBIO' => 'mbi', 'MD03G1217600' => 'mdo', 'MD05G1326200' => 'mdo', 'MD09G1096700' => 'mdo', 'MD10G1304100' => 'mdo', 'MD11G1235400' => 'mdo', 'MD17G1085000' => 'mdo', 'Medtr2g081140' => 'mtr', 'Medtr2g089995' => 'mtr', 'Medtr4g091470' => 'mtr', 'MELO3C007326.2' => 'cme', 'MELO3C013539.2' => 'cme', 'MELO3C018183.2' => 'cme', 'Migut.H01522' => 'egut', 'Migut.M01221' => 'egut', 'Migut.M01854' => 'egut', 'MSTRG.13177' => 'ama', 'MSTRG.14384' => 'ama', 'MSTRG.15200' => 'ama', 'MSTRG.15939' => 'ama', 'MSTRG.6855' => 'ama', 'MSTRG.7280' => 'ama', 'Nitab4.5_0000092g0300' => 'nta', 'Nitab4.5_0000297g0180' => 'nta', 'Nitab4.5_0000649g0050' => 'nta', 'Nitab4.5_0001386g0030' => 'nta', 'Nitab4.5_0002791g0040' => 'nta', 'Nitab4.5_0005389g0050' => 'nta', 'Nitab4.5_0009110g0020' => 'nta', 'Nitab4.5_0012449g0020' => 'nta', 'Nn1g03872' => 'nnu', 'Nn1g06784' => 'nnu', 'Oeu006767.1' => 'oeu', 'Oeu014714.1' => 'oeu', 'Oeu030438.1' => 'oeu', 'Oeu038208.1' => 'oeu', 'Oeu043687.1' => 'oeu', 'Oeu051332.1' => 'oeu', 'Oeu055687.2' => 'oeu', 'Oeu059556.1' => 'oeu', 'Os07g0558800' => 'osa', 'Os08g0141300' => 'osa', 'Peaxi162Scf00000g07614' => 'pax', 'Peaxi162Scf00007g02536' => 'pax', 'Peaxi162Scf00779g00113' => 'pax', 'Peaxi162Scf01216g00069' => 'pax', 'PGR004G2061' => 'pgr', 'PGR083G0694' => 'pgr', 'PGR142G3172' => 'pgr', 'PGSC0003DMG400018374' => 'stu', 'PGSC0003DMG400019024' => 'stu', 'PGSC0003DMG400019246' => 'stu', 'PGSC0003DMG400022352' => 'stu', 'Phvul.002G221100' => 'pvu', 'Phvul.005G107900' => 'pvu', 'Phvul.006G192600' => 'pvu', 'Phvul.011G111000' => 'pvu', 'Phvul.L001662' => 'pvu', 'Potri.001G408200' => 'ptr', 'Potri.004G033500' => 'ptr', 'Potri.011G041900' => 'ptr', 'Potri.011G126200' => 'ptr', 'Potri.013G147800' => 'ptr', 'Potri.019G116400' => 'ptr', 'Pp3c18_9820' => 'ppa', 'Pp3c21_16180' => 'ppa', 'Pp3c22_2860' => 'ppa', 'Pp3c9_14090' => 'ppa', 'Prupe.3G230200' => 'ppe', 'Prupe.4G035500' => 'ppe', 'Prupe.4G191600' => 'ppe', 'Psat5g247200' => 'psa', 'Psat5g269440' => 'psa', 'Psat7g107800' => 'psa', 'PSO210G4260' => 'pso', 'PSO541G0618' => 'pso', 'PSO675G9220' => 'pso', 'PSO832G0393' => 'pso', 'QL05p081090' => 'qlo', 'QL08p017512' => 'qlo', 'QL08p037107' => 'qlo', 'RcHm_v2.0_Chr2g0097701' => 'rch', 'RcHm_v2.0_Chr2g0161541' => 'rch', 'RcHm_v2.0_Chr5g0006131' => 'rch', 'RcHm_v2.0_Chr5g0036131' => 'rch', 'RcHm_v2.0_Chr6g0292791' => 'rch', 'Rhsim02G0119300' => 'rsi', 'RhsimUnG0258100' => 'rsi', 'Sabra04G0019300' => 'sbr', 'Sabra11G0028700' => 'sbr', 'Sabra11G0111300' => 'sbr', 'Sabra13G0119400' => 'sbr', 'Sabra16G0271300' => 'sbr', 'Sabra19G0117400' => 'sbr', 'Sabra19G0136300' => 'sbr', 'SalBow7G0147' => 'sbo', 'SalBow7G1214' => 'sbo', 'SalBow7G2949' => 'sbo', 'SalBow8G2611' => 'sbo', 'Sc03g0009550' => 'sci', 'Sc05g0008110' => 'sci', 'Sc05g0009950' => 'sci', 'Sc17g0006680' => 'sci', 'Sc21g0002540' => 'sci', 'Sed0002390' => 'sed', 'Sed0014358' => 'sed', 'Sed0016738' => 'sed', 'Sed0020771' => 'sed', 'Sed0022057' => 'sed', 'SEGI_02010' => 'sgi', 'SEGI_08362' => 'sgi', 'SEGI_14124' => 'sgi', 'SEGI_15705' => 'sgi', 'SEGI_30010' => 'sgi', 'SEGI_41076' => 'sgi', 'SGA_v2.0_scaffold114G31988' => 'sas', 'SGA_v2.0_scaffold34G13711' => 'sas', 'SGA_v2.0_scaffold73G24322' => 'sas', 'SGA_v2.0_scaffold7G03931' => 'sas', 'SHI02131' => 'shi', 'SMO165G0079' => 'smo', 'SMO367G0066' => 'smo', 'Solyc02g079230.3' => 'sly', 'Solyc07g054740.3' => 'sly', 'Solyc07g063630.3' => 'sly', 'Solyc12g005390.2' => 'sly', 'Sopen02g024050' => 'spe', 'Sopen07g028670' => 'spe', 'Sopen07g031810' => 'spe', 'Sopen12g001360' => 'spe', 'Sp6g03910' => 'spa', 'Sp6g16140' => 'spa', 'Sp7g19580' => 'spa', 'TAR624G1131' => 'tar', 'TAR626G1416' => 'tar', 'TAR627G0496' => 'tar', 'TAR629G1051' => 'tar', 'THA.LOC104799904' => 'tha', 'THA.LOC104806272' => 'tha', 'THA.LOC104812686' => 'tha', 'THA.LOC104813398' => 'tha', 'Thecc.02G171300' => 'tca', 'Thecc.06G200900' => 'tca', 'Thecc.07G070100' => 'tca', 'Thhalv10014374m.g' => 'esa', 'Thhalv10025857m.g' => 'esa', 'TPR.G15381' => 'tpr', 'TPR.G27115' => 'tpr', 'TPR.G32848' => 'tpr', 'TPR.G3918' => 'tpr', 'TWI18G0388' => 'twi', 'TWI38G0642' => 'twi', 'TWI38G1921' => 'twi', 'TWI38G1968' => 'twi', 'TWI63G0743' => 'twi', 'TWI75G0202' => 'twi', 'unitig_21.g20226' => 'ugi', 'unitig_744.g24530' => 'ugi', 'unitig_749.g13636' => 'ugi', 'vmacro09570' => 'vma', 'VMungo0251G3656' => 'vmu', 'VMungo0540G0974' => 'vmu', 'VMungo1080G1515' => 'vmu', 'VMungo1080G1825' => 'vmu', 'VMungo1127G0747' => 'vmu', 'Zm00001eb172980' => 'zma', 'Zm00001eb175260' => 'zma', 'Zm00001eb416660' => 'zma' ) $gf_id = 'HOM05D001554' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001554' ) $data_identifier = 'HOM05D001554' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 1, '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) 4, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 13, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 8, 'nnu' => (int) 2, 'oeu' => (int) 8, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 3, 'rch' => (int) 5, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416660' $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